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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGCAAGGTGTACAAAGATCATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatgctcgtgtcatttttctcatctcatgccacctagaatttgtgcagctttttatgccttgtaatgaatcctgcag

Basic information

species Zea mays
transcript GRMZM2G181359_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g54340.2 (Oryza sativa), 5'ss of exon 4
GTGGCAAGGTGTACAAAGATCATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatgctcgtgtcatttttctcatctcatgccaccta-------gaatttgtgcagc---tttttatgccttgtaatgaatcctgcag
||||| |||||||| ||||| ||||| |||||||| |||||||| |||||||| || |||||||||||||| ||||| |||| |||||||  |   |||||  | |   |||  |    |        ||| |||  | |   || | || |  | |  || ||| | |||
GTGGCTAGGTGTACCAAGATTATAAGTCCTAATACTGATGATGCTAAATATGTGATTAATGTAAAACAAATTGCAAAGgtattccatgcttatccaattttattgaaaccatatctttcatgaaaaaaaatgtgttgatccctttctcatactgtattttgtatcattcag

upper sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA19G45140.1 (Glycine max), 5'ss of exon 4
GTGGCAAGGTGTACAAAGATCATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatgctcgtgtcatttttctca---tctcatgccacctagaatttgtgcagctt-tttatgccttgtaatgaatcctgcag--------------------------------------------------------------------------------------------------------------
|| |||||||| |||||||||||||  || ||| | || ||||||||||||||||| ||||| || || || ||||| |||  | ||  |     || | |    |   |  ||  |   |      ||   || |   ||||| |  | |  |   |  || ||                                                                                                              
GTAGCAAGGTGCACAAAGATCATAAATCCAAATTCAGAAGATGCCAAATATGTTATCAATGTGAAGCAGATTGCAAAGgtaatctatattttcaacaatgtgaagaagatgccaaactgtcccattgtttctcaccacatttatcctatattcttggtt-tgaagatgttagacttcacttactgttatgaaattgtcaatgggttggcaaagctgttgattcttttctttatgctgtcaggactaataatccttctgcgttctttttatgacag

upper sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA07G05220.1 (Glycine max), 5'ss of exon 4
GTGGCAAGGTGTACAAAGATCATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgc-catgctcgtgtcatttttctcatctcatgccacctagaatt--tgtgcagctttttatgcct-tgtaatgaatcctgcag-------------
||||||||||| |||||||| |||| ||| ||| | || |||||||| |||||||| ||||| || || || ||||| ||      ||  | || | ||     || | ||||    ||  ||  |       || | |||     | | |       | ||                
GTGGCAAGGTGCACAAAGATTATAAACCCAAATTCTGAAGATGCCAAGTATGTTATCAATGTGAAGCAGATTGCAAAGgtgcctatatttttgtttaataacaatcttttcatatttccctgatctatcagatagttgtttgaatatatctggcatcacttgttaatcaagatatttc

upper sequence: GRMZM2G181359_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv09s0002g00170.t01 (Vitis vinifera), 5'ss of exon 4
GTGGCAAGGTGTACAAAGATCATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatgctcgtgtcatttt-tctcatctcat-gccacctagaatttgtgcagctttttatgccttgtaatgaatcctgcag---------------
|||||||| || |||||||| || ||||| ||| | || |||||||||||||| |||||||| |||||||| ||||| ||| ||     |  |   | | | | || ||  || |  || |  ||    || |  || || | |  |    |   |  ||                  
GTGGCAAGATGCACAAAGATAATTAGCCCCAATTCTGAGGATGCCAAATATGTGATAAATGTTAAACAAATTGCAAAGgtaagcttcaattttaagactctgtttcttcctatagaaacttgtaaagcatggactttctttttctgttccttttgttttgttcaaacgcaaaattttt

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|31998161|gb|CD661959.1|CD661959
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|148939474|gb|EC884049.2|EC884049
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|32909117|gb|CF013929.1|CF013929
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|148930441|gb|EE284947.2|EE284947
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|148986522|gb|EE030276.2|EE030276
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|148941059|gb|EC885918.2|EC885918
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|28987578|gb|CB351704.1|CB351704
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|148940274|gb|EC885053.2|EC885053
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|211087536|gb|FL161883.1|FL161883
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGG
EST: gi|149102256|gb|EE287643.2|EE287643
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|148940455|gb|EC885254.2|EC885254
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|148981623|gb|EE027766.2|EE027766
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|26457221|gb|CA828804.1|CA828804
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|149078548|gb|EE167330.2|EE167330
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|211087533|gb|FL161880.1|FL161880
EST:     -TAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTTGTTGTTGGACTNNNNNNNATAAAGTGTCTCCAACTGACATCGAG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTT-GTTGTTGGACTGGGGG--ATAAAGTGTCTCCAACTGACATCGAG
EST: gi|211087537|gb|FL161884.1|FL161884
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGGTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|148933068|gb|EE285985.2|EE285985
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|67042393|gb|CO468648.1|CO468648
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|149004352|gb|EE039050.2|EE039050
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCG
EST: gi|148943018|gb|EC888066.2|EC888066
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCANAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|148952264|gb|EC898073.2|EC898073
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|60401248|gb|DN234055.1|DN234055
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|149077295|gb|EE165971.2|EE165971
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|211087539|gb|FL161886.1|FL161886
EST:     AATACGGATGATGCCNAATATGTTATAAATTGTAAAACCANATCGCAAAA                         TTTGTTGTTGGACTGG
genomic: AATACGGATGATGCCAAATATGTTATAAAT-GTAAAACAA-ATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGG
EST: gi|148968071|gb|EE019406.2|EE019406
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
EST: gi|149040621|gb|EE046862.2|EE046862
EST:     CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAA                         TTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG
genomic: CTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 254

GTGGCAAGGTGTACAAAGATCATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 224

GTGGCAAGGTGTACAAAGATCATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 212

GTGGCAAGGTGTACAAAGATCATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG


Block sizes: 39 (upstream exon), 46 (downstream exon)
Score: 210

GTGGCAAGGTGTACAAAGATCATAAGCCCTAATACGGATGATGCCAAATATGTTATAAATGTAAAACAAATCGCAAAAgtatgccatg ... aatcctgcagTTTGTTGTTGGACTGGGGGATAAAGTGTCTCCAACTGACATCGAGGAAGGGATGAGGGTCGG